sgRNA Scorer 2.0

Welcome to sgRNA Scorer 2.0. In this version, we combined the support vector machine models for Cas9 S. pyogenes and Cas9 S. thermophilus 1 into a single pan-ortholog model and have demonstrated experimentally that it works with varying degree of success for Cas9s from S. aureus and S. thermophilus 3 as well as the newly characterized CRISPR system Cpf1. The standalone version of this software can be found here and the user manual on how to use our tools can be found here.

Given an input sequence or list of sequences as well as a CRISPR system with a defined spacer length and PAM sequence, our interactive web tool will identify putative sites and assign a predicted activity based on our new support vector machine model. In addition, an option exists to select sites with minimal off-target activity based on the CasFinder algorithm as well, enabling target sites to be selected with high predicted specificity and activity.

From our original paper, human and mouse exome wide lists for Cas9 Sp and St1 can be found here.

Please use a working e-mail address as a link to a file with results from sgRNA scorer will be emailed to you as soon as it's done. The file will be retained for 24 hours. If you have not received an email within 24hrs with a link to your results, please email to let us know so that we can fix the issue.


E-mail address:

CRISPR system:

Spacer length (14-24): PAM sequence (e.g. NGG): PAM orientation:

Select input (paste sequence or upload file, FASTA format, limit to 1 Mb of sequence total). Sequence must be at least 30 nucleotides in length.

Paste sequence

Upload file
Run CasFinder off-target analysis?

Citing our tool:
Chari R, Yeo N, Chavez A, Church GM (2017). sgRNA Scorer 2.0 – a species independent model to predict CRISPR/Cas9 activity. ACS Synthetic Biology. Accepted.

If you use the CasFinder functionality as well, please cite:
Aach J, Mali P, Church GM (2014). CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes. BioRxiv.

The standalone version of this software can be found here.

Any suggestions or comments can be e-mailed to sgRNAScorer 'at' hms 'dot' harvard 'dot' edu

Updated February 1st, 2017